How to Generate tissue_lowres_image.png from tissue_hires_image.png for spatial transcriptomics?

Question

[Genomancer]

Hi everyone,

I’m working with spatial transcriptomics data in Seurat but only have these files:

filtered_feature_bc_matrix.h5 
tissue_hires_image.png
tissue_positions_list.csv
scalefactors_json.json

I need to generate tissue_lowres_image.png because my system can’t handle the high-res image because I'm working with multiple tissues, is there a tutorial on how to downscale tissue_hires_image.png or how to create the tissue_hires_image.png?

Either Python or R will be fine

Answer 1

[GenoMax]

Is this 10x spatial data? File names seem to indicate so. While someone provides an answer this is what 10x support says about the tissue images.

https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs

my system can’t handle the high-res image because I'm working with multiple tissues

As in you don't have enough memory?

It looks like Seurat can handle high-res images based on this comment --> https://github.com/satijalab/seurat/issues/5614#issuecomment-2105263800 but that is likely not the question you are asking.

[Genomancer]

sorry for the incomplete question. Yes, its 10x spatial data and I'm having trouble comparing the multiple tissues because I don't have enough memory I used the calculations in the 10x support in the link you provided and I was able to solve the problem. thanks